Biomedicine

Creating Cell Parts from Scratch

A newly made synthetic ribosome is an important step in the quest to create artificial life forms.

Researchers at Harvard University have built a functional ribosome–the cell’s protein-making machine–from scratch, molecule by molecule. The creation represents a significant step toward making artificial life, and it could ultimately fill a major gap in our understanding of the origins of life. But the scientists who made the ribosome are most interested in its industrial applications. They plan to genetically tinker with the molecular machinery so that it can make proteins more efficiently, as well as proteins that are the mirror image of those ordinarily found in nature. Both improvements could be a major advantage in the pharmaceutical industry, among others.

Protein factory: Shown here is the structure of a ribosome, the cellular structure that produces proteins. Scientists have now created a ribosome from scratch.

To make the ribosomes, George Church, a Harvard geneticist, and postdoctoral researcher Mike Jewett first disassembled ribosomes from Escherichia coli, a common lab bacterium, into its component molecules. They then used enzymes to put the various RNA and protein components back together. When put together in a test tube, these components spontaneously formed into functional ribosomes. While scientists have previously reconstituted ribosomes, which are made up of a complex configuration of RNA and proteins, as far back as the 1960s, these earlier versions were poor protein producers, and were created under chemical conditions very different than that of a normal cell.

The researchers used the artificial ribosome to successfully produce the luciferase enzyme, a firefly protein that generates the bug’s glow. Eventually, says Church, he wants to create tiny protein factories out of tailor-made ribosomes. “We want to make large amounts of special proteins that are hard to make in vivo, and are useful for vaccine production [and other purposes].”

Next, the researchers want to create a ribosome that can re-create itself. They have compiled a list of 151 genes that they think are needed for a self-reproducing ribosome, including genes for ribosomal proteins, different types of RNAs, enzymes that catalyze different reactions in protein synthesis, and additional genes not directly related to the ribosome. “We think this is enough genes to replicate DNA, produce RNA and ribosomes, and have a primitive membrane,” says Church.”Once you get it going, it should be able to keep going if you supply it with amino acids and nucleotides [the building blocks of DNA and RNA].”

Once they get the system up and running, the researchers hope to genetically optimize it into an efficient protein factory. Protein products, such as biologic drugs, are now mostly made in vats of bacteria. “When you make proteins in live bacteria, you throw away 90 percent of the bacterial biomass just to get a few grams of protein,” says David Deamer, a chemist at the University of California, Santa Cruz. “If you could do it without live organisms, it could be much more efficient.”

Reconstituting ribosomes: Shown here is a parts list for creating a synthetic, self-replicating ribosome. Proteins are shown in purple, RNA in red, and DNA in blue. The list includes 54 ribosomal proteins, as well as RNA-based enzymes involved in protein production, and other molecules that interact with ribosomes.

Church and his team also want to use the ribosome to make a new class of proteins–those that are the mirror image of the proteins found in nature. Proteins and many other molecules have a “handedness,” or chirality, to their structure. Amino acids made in nature are almost exclusively left-handed. And just as a glove fits on only one hand, left-handed enzymes can only catalyze reactions of substrates with the correct handedness. This means that mirror-image molecules would be resistant to breakdown by regular enzymes, says Church. That could have important industrial applications, generating long-lasting enzymes for biofermentation, used to create biofuels and other products.

The pharmaceutical industry might also benefit from a method to make mirror-image molecules. Unlike biological synthesis, chemical synthesis produces a mixture of left- and right-handed molecules. But with many drugs–the most notorious example is thalidomide–one form is beneficial and the other harmful. It’s expensive to separate the two versions, so an efficient alternative that makes just the desired form from the start could be a boon to manufacturers. Church and Jewett have not yet made a mirror-image protein using their synthetic ribosome, but they say that it can be done just by tweaking a few molecules in the enzyme that joins amino acids into proteins.

The artificial ribosome also has much broader applications. It is a major step on the way to creating artificial life–a cell that can self-assemble and reproduce. Scientists want to create an organism from scratch both to better understand the inner workings of biology and to create new, highly engineerable life forms that can be employed to make new fuels, clean up toxins, or perform other useful functions.

In addition, the ribosome might solve major unanswered questions about the origins of life. “How did the first ribosomes or the equivalent structure evolve on the way to life as we know it? This is really a major gap in our understanding of the origin of life,” says Deamer. “If [Church] can manipulate parts to make a better or simpler version of the ribosome, it will teach us a lot about how ribosomes came to be.” And second, why does almost all life have a left-handed chirality? “It’s a mystery,” says Fred Blattner, a geneticist at the University of Wisconsin-Madison. “Did it just happen that way, or is there a reason we are not aware of?” With a left-handed ribosome, the answer to the question may soon be in reach.

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